每天学习一点R：17.barplot条形图之带误差棒的对称条形图

今天继续进行基于barplot()命令的文章条形图仿制，今天会重点介绍在R中如何绘制对称的条形图以及怎么给条形添加误差棒。

原图展示

之前看过一篇利用肠道菌群进行疾病诊断的文章，其中涉及到一个图形，作者将筛选出的marker微生物的总丰度与肠道菌群的alpha多样性指数在同一个图像利用对称的条形图进行展示，同时给出了健康和疾病样品间的差异检验结果。

今天就来仿照绘制一下这幅图，我绘制出来的最终图像是下面这个样子。

还是照例先给出完成的绘图代码：

marker_abundance <- read.table("marker_abundance.txt",header = TRUE,row.names = 1,sep = "\t")
diversity <- read.table("index.txt",header = TRUE,row.names = 1,sep = "\t")

library(ggplot2)

tiff(filename = "marker_abundance_diversity.tif",width = 5400,height = 7200,compression = "lzw",res = 600,type = "windows")
par(mfrow = c(2,1))
par(mar = c(5,7,1,1))
par(xpd = TRUE)
bar1 <- barplot(marker_abundance$Abundance,ylim = c(0,0.9),axes = FALSE,col = "grey80")
axis(side = 2,at = c(0,0.2,0.4,0.6,0.8),labels = c("","","","",""),lwd = 3)
text(x = 0.07,y = c(0,0.4,0.8),labels = c(0,0.4,0.8),cex = 2.5,adj = c(1,0.5))
mtext(side = 2,text = "Abundance sum",line = 4,cex = 3)
arrows(x0 = 0.7,y0 = 0.4478635,x1 = 0.7,y1 = 0.4478635+0.05248740,col = "black",angle = 90,length = 1,lwd = 3)
arrows(x0 = 1.9,y0 = 0.4721783,x1 = 1.9,y1 = 0.4721783+0.07471587,col = "black",angle = 90,length = 1,lwd = 3)
text(x = bar1,y = -0.12,labels = c("Disease","Healthy"),cex = 3.5)
segments(x0 = 0.7,y0 = 0.55,x1 = 0.7,y1 = 0.75,col = "black",lwd = 3)
segments(x0 = 0.7,y0 = 0.75,x1 = 1.9,y1 = 0.75,col = "black",lwd = 3)
segments(x0 = 1.9,y0 = 0.75,x1 = 1.9,y1 = 0.58,col = "black",lwd = 3)
text(x = 1.3,y = 0.8,labels = "NS",cex = 2.5)
bar2 <- barplot(diversity$shannon,ylim = c(-12,0),axes = FALSE,col = "grey80")
axis(side = 2,at = c(-12,-10,-8,-6,-4,-2,0),labels = c("","","","","","",""),lwd = 3)
text(x = 0.07,y = c(-12,-8,-4,0),labels = c(-12,-8,-4,0),cex = 2.5,adj = c(1,0.5))
mtext(side = 2,text = "Within-sample diversity",line = 4,cex = 3)
arrows(x0 = 0.7,y0 = -8.946364,x1 = 0.7,y1 = -8.946364-0.5686171,col = "black",angle = 90,length = 1,lwd = 3)
arrows(x0 = 1.9,y0 = -8.716364,x1 = 1.9,y1 = -8.716364-0.6158940,col = "black",angle = 90,length = 1,lwd = 3)
segments(x0 = 0.7,y0 = -10,x1 = 0.7,y1 = -12,col = "black",lwd = 3)
segments(x0 = 0.7,y0 = -12,x1 = 1.9,y1 = -12,col = "black",lwd = 3)
segments(x0 = 1.9,y0 = -12,x1 = 1.9,y1 = -9.8,col = "black",lwd = 3)
text(x = 1.3,y = -13,labels = "NS",cex = 2.5)
dev.off()

绘制这个图像需要两个数据，一个是marker微生物总丰度，另一个是样品对应的alpha多样性指数，需要在绘图前先使用Excel分别计算实验和对照组中marker微生物总丰度和alpha多样性指数的平均值和标准偏差(sd)，具体的绘图数据如下：

特别需要注意的是：用于绘制下方条形图的数据要手动改为负值，sd不需要改为负值。

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绘图过程详解

定义绘图区域

首先要制定用于绘图的区域。

par(mfrow = c(2,1))

将绘图区定义为两行一列，分别用于绘制两个互相对称的条形图。

par(mar = c(5,7,1,1))

指定第一个绘图区即上方条形图的绘图边界，注意下方和左侧要留出大一点的区域，用于样品组的名称和纵坐标，而上方和右侧的边界要尽量小。

第二个绘图区即下方条形图的绘图边界无需设置。

par(xpd = TRUE)

将绘图参数定义为可以在绘图区外显示，从而使得绘图参数的显示能够跨越上下两个绘图区。

上方条形图绘制

定义完绘图区之后，要首先进行上方条形图的绘制。

bar1 <- barplot(marker_abundance$Abundance,
ylim = c(0,0.9),axes = FALSE,col = "grey80")

注意：y轴的范围要适当的大一些，为差异性检验结果的展示预留空间。

使用“axes = FALSE”隐藏默认的坐标轴信息。

axis(side = 2,at = c(0,0.2,0.4,0.6,0.8),
labels = c("","","","",""),lwd = 3)

添加纵坐标，并将刻度标签设为空。

text(x = 0.07,y = c(0,0.4,0.8),
labels = c(0,0.4,0.8),cex = 2.5,
adj = c(1,0.5))

通过x的数值，调整标签与坐标轴刻度的间距。

添加纵坐标刻度标签，通过标签的数量和间隔实现坐标轴的主刻度和副刻度。

使用adj参数调整标签的对齐方式，使得长度不一的标签文本统一靠右居中对齐。

mtext(side = 2,text = "Abundance sum",
line = 4,cex = 3)

添加纵坐标轴的标签，使用line参数调整标签与坐标轴的距离，cex调整标签字号的大小。

条形误差棒的添加

R默认的绘图命令中并不包含误差棒的绘制，这里使用arrows()命令以箭头的形式添加误差棒。

arrows(x0 = 0.7,y0 = 0.4478635,
x1 = 0.7,y1 = 0.4478635+0.05248740,
col = "black",angle = 90,length = 1,lwd = 3)

arrows(x0 = 1.9,y0 = 0.4721783,
x1 = 1.9,y1 = 0.4721783+0.07471587,
col = "black",angle = 90,length = 1,lwd = 3)

箭头的x0位对应条形在x轴的位置，因为是竖直方向的，因而x1与x0一致。

y0为对应条形的绘图数值，y1为绘图数值+sd。

angle设置为90度，使得箭头的两边处于一条水平的直线，从而形成误差棒的形式。

使用length和lwd调整误差棒的长度和线宽。

差异性检验结果展示

使用线段的形式构成一个U型框连接两个条形，之后利用文本给出组间差异性检验结果。

segments(x0 = 0.7,y0 = 0.55,x1 = 0.7,y1 = 0.75,col = "black",lwd = 3)
segments(x0 = 0.7,y0 = 0.75,x1 = 1.9,y1 = 0.75,col = "black",lwd = 3)
segments(x0 = 1.9,y0 = 0.75,x1 = 1.9,y1 = 0.58,col = "black",lwd = 3)
text(x = 1.3,y = 0.8,labels = "NS",cex = 2.5)

具体的参数数值根据绘图数据进行调整。

此时需要添加条形对应的样本组名称，因为如果在第二个条形绘制后再添加可能需要额为设置绘图区参数。

text(x = bar1,y = -0.12,
labels = c("Disease","Healthy"),
cex = 3.5)

注意：在第二个条形绘制完成之后，再返回此处调整标签在y轴的位置，使得标签位于两个条形图的中间。

对称条形的绘制

对称条形的绘制方法与第一个条形图基本一致。

bar2 <- barplot(diversity$shannon,ylim = c(-12,0),axes = FALSE,col = "grey80")
axis(side = 2,at = c(-12,-10,-8,-6,-4,-2,0),labels = c("","","","","","",""),lwd = 3)
text(x = 0.07,y = c(-12,-8,-4,0),labels = c(12,8,4,0),cex = 2.5,adj = c(1,0.5))
mtext(side = 2,text = "Within-sample diversity",line = 4,cex = 3)
arrows(x0 = 0.7,y0 = -8.946364,x1 = 0.7,y1 = -8.946364-0.5686171,col = "black",angle = 90,length = 1,lwd = 3)
arrows(x0 = 1.9,y0 = -8.716364,x1 = 1.9,y1 = -8.716364-0.6158940,col = "black",angle = 90,length = 1,lwd = 3)
segments(x0 = 0.7,y0 = -10,x1 = 0.7,y1 = -12,col = "black",lwd = 3)
segments(x0 = 0.7,y0 = -12,x1 = 1.9,y1 = -12,col = "black",lwd = 3)
segments(x0 = 1.9,y0 = -12,x1 = 1.9,y1 = -9.8,col = "black",lwd = 3)
text(x = 1.3,y = -13,labels = "NS",cex = 2.5)

需要注意的是：

1. 对称条形图因为是在下方展示，所以所有的数值均是负数；

2. 在绘制下方条形图纵坐标标签时，要将标签设置为对应的正数；

3. 由于此时误差棒的方向是向下，因而y1的数值为mean-sd。

扩展阅读

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